Hi Sean,
Just back from holiday and 'catching up' with the Forum.
The first SDR dongle plugged into PAW will be programmed automatically to 1090MHz. When a second SDR dongle is then plugged in, this one will be automatically programmed to 978MHz. AFAIK the system will then treat them the same each time it boots up, but Lee would need to confirm this. (With a 'shared antenna' of course it doesn't matter which SDR gets tuned to which frequency *).
Do NOT 'set up' SD to receive weather - the weather settings in SD are intended for use when using the internet to provide weather data. WRT 978MHz - it is supposed to 'just work' when the GDL90 protocol is selected and appropriate data is received (though with only one flight 'Down South' since the Wx trials started, my personal experience here is 'limited'). Changing protocol back to PilotAware (UDP) will revert to 'normal' traffic.
BTW, I have said previously in another thread that I had concerns initially about the loss of 'Visual' on-screen 'Bearingless Target Alerts' when using GDL90, but in practice during a fairly long flight from Popham round the South Coast and back up the East side of London, I found that having to use the audio alerts alone definitely proved less 'distracting' and encouraged better external scanning to find the reported aircraft as opposed to looking 'on-screen' - provided you don't miss the relative altitude in the initial audio report.
Best Regards as always
Peter
* p.s. If using a single antenna, and Wx is a priority, the current thinking is to use an antenna tuned to 978MHz and preferably with a bit of 'gain' (e.g. 5dBi) as this will give the best chance of receiving reliable Wx data, whereas the much stronger 1090MHz signals are much less critical.